Quick Glimpse

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Cover Image

Structure of this guide

This is an example report showing the major parts of microbiome data analysis workflows.






Mothur Microbiome Snakemake Workflow

We use snakemake [@Dadasnake2021] to maintain reproducibility and improvement of the bioinformatics analysis of microbiome data.


Example of common FAQs (in progress)

  1. Mothur dist.seqs taking too long.
    • Length of the merged reads (merged reads over 300pb).
    • Not enough overlaping when merging the paired reads.
    • Use other pre-cluster algorithm like Deblur.
    • Too many uniques?
    • Not enough computer power?: Use HPC or Cluster.
    • Try to make contigs using maxee instead of deltaq or use phylogeny approach for downstream analysis, or use clister.split based on taxonomy.
    • do not forget to use controls.





References